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GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis. ​

文献信息 ​

DOI10.1093/nar/gkz430
PMID31114875
期刊Nucleic acids research
影响因子13.1
JCR 分区Q1
发表年份2019
被引次数2645
关键词基因表达分析, 癌症亚型, 转录组数据
文献类型Journal Article, Research Support, Non-U.S. Gov't
ISSN0305-1048
页码W556-W560
期号47(W1)
作者Zefang Tang, Boxi Kang, Chenwei Li, Tianxiang Chen, Zemin Zhang

一句话小结 ​

GEPIA2是基于GEPIA的更新版本，提供更高分辨率的基因表达分析，展示了198,619个异构体和84种癌症亚型，支持用户上传RNA-seq数据进行比较分析。该平台的增强功能和新技术使其成为癌症研究中更为重要的工具，推动了基因表达研究的深入发展。

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基因表达分析 · 癌症亚型 · 转录组数据

摘要 ​

在2017年推出的GEPIA（基因表达谱交互分析）网络服务器，已成为基于TCGA和GTEx数据库中肿瘤及正常样本的基因表达分析的重要且被广泛引用的资源。在此，我们介绍GEPIA2，这是一个更新和增强的版本，旨在提供更高分辨率和更多功能的洞察。GEPIA2展示了198,619个异构体和84种癌症亚型，扩展了基因表达定量的范围，从基因层面到转录本层面，并支持对特定癌症亚型的分析以及亚型之间的比较。此外，GEPIA2还采用了受单细胞测序研究启发的新基因特征定量分析技术，并提供定制化分析，用户可以上传自己的RNA-seq数据并与TCGA和GTEx样本进行比较。我们还提供API以便进行批量处理和便捷检索分析结果。更新后的网络服务器可以通过http://gepia2.cancer-pku.cn/公开访问。

英文摘要 ​

Introduced in 2017, the GEPIA (Gene Expression Profiling Interactive Analysis) web server has been a valuable and highly cited resource for gene expression analysis based on tumor and normal samples from the TCGA and the GTEx databases. Here, we present GEPIA2, an updated and enhanced version to provide insights with higher resolution and more functionalities. Featuring 198 619 isoforms and 84 cancer subtypes, GEPIA2 has extended gene expression quantification from the gene level to the transcript level, and supports analysis of a specific cancer subtype, and comparison between subtypes. In addition, GEPIA2 has adopted new analysis techniques of gene signature quantification inspired by single-cell sequencing studies, and provides customized analysis where users can upload their own RNA-seq data and compare them with TCGA and GTEx samples. We also offer an API for batch process and easy retrieval of the analysis results. The updated web server is publicly accessible at http://gepia2.cancer-pku.cn/.

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主要研究问题 ​

  1. GEPIA2在处理特定癌症亚型的表达分析时，采用了哪些新的分析技术？
  2. 如何利用GEPIA2进行自定义RNA-seq数据的上传和比较？
  3. GEPIA2与之前版本相比，在功能和分辨率上有哪些显著提升？
  4. 在使用GEPIA2进行基因签名量化时，单细胞测序研究的启发具体体现在哪些方面？
  5. GEPIA2的API功能如何支持批量处理和分析结果的检索？

核心洞察 ​

研究背景和目的 ​

GEPIA（Gene Expression Profiling Interactive Analysis）是一个基于TCGA（癌症基因组图谱）和GTEx（基因型-组织表达）数据库的基因表达分析工具。2019年，GEPIA的更新版本GEPIA2被推出，旨在提供更高分辨率的表达分析和更多功能，支持对198,619个转录本和84种癌症亚型的分析。GEPIA2的目标是帮助研究人员更深入地理解癌症的基因表达特征和相关机制。

主要方法/材料/实验设计 ​

GEPIA2的功能分为两大类：表达分析和自定义数据分析。其主要功能包括：

  1. 表达分析：

    • 生存分析：基于基因或转录本表达水平进行生存分析。
    • 差异基因分析：识别不同样本间的表达差异。
    • 转录本详细信息：分析特定转录本的表达分布。
    • 相关性分析：探索基因间的相关性。
    • 相似基因检测：寻找功能相似的基因。
    • 降维分析：通过降维技术可视化数据。

  2. 自定义数据分析：

    • 癌症亚型分类器：基于用户上传的表达数据预测癌症类型或亚型。
    • 表达比较：将用户数据与TCGA和GTEx数据进行比较。

以下是GEPIA2的技术路线流程图（Mermaid代码）：

Mermaid diagram

关键结果和发现 ​

  • GEPIA2扩展了对转录本水平的分析，使得用户能够研究不同转录本在癌症中的特异性表达。
  • 通过生存分析功能，用户可以评估特定基因或转录本在不同癌症类型中的预后影响。
  • GEPIA2允许用户上传自己的RNA-seq数据，并与TCGA和GTEx数据进行比较，极大地方便了个性化分析。

主要结论/意义/创新性 ​

GEPIA2的推出显著增强了GEPIA的功能，使其成为生物医学研究人员和临床医生在癌症基因组数据探索中的重要工具。其新功能如转录本使用分析和自定义数据分析为用户提供了更高分辨率的分析能力，推动了癌症研究的深入发展。

研究局限性和未来方向 ​

尽管GEPIA2提供了丰富的功能，但仍存在一些局限性，例如数据处理的速度和用户界面的复杂性。未来的方向包括进一步优化数据处理速度、扩展分析功能和增强用户体验。此外，考虑整合更多的多组学数据，以提供更全面的癌症生物学视角。

参考文献 ​

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引用本文的文献 ​

  1. Cancer biology as revealed by the research autopsy. - Christine A Iacobuzio-Donahue;Chelsea Michael;Priscilla Baez;Rajya Kappagantula;Jody E Hooper;Travis J Hollman - Nature reviews. Cancer (2019)
  2. More Than an Adipokine: The Complex Roles of Chemerin Signaling in Cancer. - Kerry B Goralski;Ashley E Jackson;Brendan T McKeown;Christopher J Sinal - International journal of molecular sciences (2019)
  3. Analysis of Promoter-Associated Chromatin Interactions Reveals Biologically Relevant Candidate Target Genes at Endometrial Cancer Risk Loci. - Tracy A O'Mara;Amanda B Spurdle;Dylan M Glubb; - Cancers (2019)
  4. Integration of Bioinformatics Resources Reveals the Therapeutic Benefits of Gemcitabine and Cell Cycle Intervention in SMAD4-Deleted Pancreatic Ductal Adenocarcinoma. - Yao-Yu Hsieh;Tsang-Pai Liu;Chia-Jung Chou;Hsin-Yi Chen;Kuen-Haur Lee;Pei-Ming Yang - Genes (2019)
  5. An Integrated Bioinformatics Analysis Repurposes an Antihelminthic Drug Niclosamide for Treating HMGA2-Overexpressing Human Colorectal Cancer. - Stephen Wan Leung;Chia-Jung Chou;Tsui-Chin Huang;Pei-Ming Yang - Cancers (2019)
  6. MiR-92a Family: A Novel Diagnostic Biomarker and Potential Therapeutic Target in Human Cancers. - Min Jiang;Xuelian Li;Xiaowei Quan;Xiaoying Li;Baosen Zhou - Frontiers in molecular biosciences (2019)
  7. High Expression of TTYH3 is Related to Poor Clinical Outcomes in Human Gastric Cancer. - Subbroto Kumar Saha;Polash Kumar Biswas;Minchan Gil;Ssang-Goo Cho - Journal of clinical medicine (2019)
  8. Expression profile analysis of two antisense lncRNAs to improve prognosis prediction of colorectal adenocarcinoma. - Milad Shademan;Azam Naseri Salanghuch;Khadijeh Zare;Morteza Zahedi;Mohammad Ali Foroughi;Kambiz Akhavan Rezayat;Hooman Mosannen Mozaffari;Kamran Ghaffarzadegan;Ladan Goshayeshi;Hesam Dehghani - Cancer cell international (2019)
  9. Bioinformatic Identification of miR-622 Key Target Genes and Experimental Validation of the miR-622-RNF8 Axis in Breast Cancer. - Chuanyang Liu;Lu Min;Jingyu Kuang;Chushu Zhu;Xin-Yuan Qiu;Lingyun Zhu - Frontiers in oncology (2019)
  10. Interleukin-18 Is a Prognostic Biomarker Correlated with CD8+ T Cell and Natural Killer Cell Infiltration in Skin Cutaneous Melanoma. - Minchan Gil;Kyung Eun Kim - Journal of clinical medicine (2019)

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